Well at that point it's meant to be they can't be reasoned with, war / fight to the death inevitable. Then at the end it's revealed they were just defending their territory.

If we have a situation where understanding is reached, communication and mutual empathy then exactly what is Kirk fighting about and learning in Arena?

It already doesn't totally work now the Gorn and their space are personally known about by most of the crew present in Arena, by Starfleet etc. but I can wave that off as being worth it for the story. But this would mean that the message of Arena is also damaged, not just continuity. Not sure how I feel about that but I'll see how they handle it first.